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Creators/Authors contains: "Franks, Peter J. S."

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  1. Abstract

    Locally enhanced biological production and increased carbon export are persistent features at oceanic density fronts. Studies often assume biological properties are uniform along fronts or hypothesize that along‐ and across‐front gradients reflect physical‐biological processes occurring in the front. However, the residence times of waters in fronts are often shorter than biological response times. Thus, an alternate—often untested—hypothesis is that observed biological patchiness originates upstream of a front. To test these two hypotheses, we explore an eddy‐associated front in the California Current System sampled during two surveys, separated by 3 weeks. Patches of high phytoplankton biomass were found at the northern ends of both surveys, and phytoplankton biomass decreased along the front. While these patches occurred in similar locations, it was unclear whether the same patch was sampled twice, or whether the two patches were different. Using an advection‐reaction framework combined with field and satellite data, we found that variations in along‐front gradients in dissolved oxygen, particle biovolume, and salinity support the conclusion that the two phytoplankton patches were different. They were only coincidentally sampled in similar locations. Backward‐ and forward‐in‐time tracking of water parcels showed that these phytoplankton patches had distinct origins, associated with specific, strong coastal upwelling pulses upstream of the front. Phytoplankton grew in these recently upwelled waters as they advected into and along the frontal system. By considering both local and upstream physical‐biological forcings, this approach enables better characterizations of critical physical and biogeochemical processes that occur at fronts across spatial and temporal scales.

     
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  2. Abstract

    In the California Current System, cross‐shore transport of upwelled, nutrient‐rich waters from the coastal margin to the open ocean can occur within intermittent, submesoscale‐to‐mesoscale features such as filaments. Time‐varying spatial gradients within filaments affect net cross‐shore fluxes of physical, biological, and chemical tracers but require high‐resolution measurements to accurately estimate. In June 2017, theCalifornia Current EcosystemLong Term Ecological Research program process cruise (P1706) conducted repeat sections by an autonomousSprayglider and a towed SeaSoar to investigate the role of one such coastal upwelling feature, the Morro Bay filament, which was characterized by enhanced cross‐filament gradients (both physical and biological) and an along‐filament jet. Within the jet, speeds were up to 0.78 m/s and the offshore transport was 1.5 Sverdrups (3.8 Sverdrups) in the upper 100 m (500 m). A climatological data product from the sustained California Underwater Glider Network provided necessary information for water mass differentiation. The analysis revealed that the cold, salty side of the filament carried recently upwelled California Undercurrent water and corresponded to higher chlorophyll‐afluorescence than the warm, fresh side, which carried California Current water. Thus, there was a convergence of heterogeneous water masses within the core of the filament’s offshore‐flowing jet. These water masses have different geographic origins and thermohaline characteristics, which has implications for filament‐related cross‐shore fluxes and submesoscale‐to‐mesoscale biological community structure gradients.

     
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  3. Abstract

    The potential influences of turbulence on planktonic processes such as nutrient uptake, grazing, predation, infection, and mating have been explored in hundreds of laboratory and theoretical studies. However, the turbulence levels used may not represent those experienced by oceanic plankton, bringing into question their relevance for understanding planktonic dynamics in the ocean. Here, we take a data‐centric approach to understand the turbulence climate experienced by plankton in the ocean, analyzing over one million turbulence measurements acquired in the open ocean. Median dissipation rates in the upper 100 m were < 10−8 W kg−1, with 99% of the observations < 10−6 W kg−1. Below mixed layers, the median dissipation rate was ~ 10−10 W kg−1, with 99% of the observations < 10−7 W kg−1. Even in strongly mixing layers the median dissipation rates rarely reached 10−5 W kg−1, decreasing by orders of magnitude over 10 m or less in depth. Furthermore, episodes of intense turbulence were transient, transitioning to background levels within 10 min or less. We define three turbulence conditions in the ocean: weak (< 10−8 W kg−1), moderate (10−8–10−6 W kg−1), and strong (> 10−6 W kg−1). Even the strongest of these is much weaker than those used in most laboratory experiments. The most frequent turbulence levels found in this study are weak enough for most plankton—including small protists—to outswim them, and to allow chemical plumes and trails to persist for tens of minutes. Our analyses underscore the primary importance of planktonic behavior in driving individual interactions.

     
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  4. Abstract

    In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet‐18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea,Chattonellaspp.,Dinophysisspp., andLingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy forA. sanguinea(),Chattonellaspp. (), andL. polyedra(), whereas models forDinophysisspp. showed lower prediction accuracy (). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional‐scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional‐scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor ofChattonellaandDinophysisspp., but not ofA. sanguineaandL. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real‐time HAB abundance forecasts.

     
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  5. Abstract

    The large data sets provided byin situoptical microscopes are allowing us to answer longstanding questions about the dynamics of planktonic ecosystems. To deal with the influx of information, while facilitating ecological insights, the design of these instruments increasingly must consider the data: storage standards, human annotation, and automated classification. In that context, we detail the design of the Scripps Plankton Camera (SPC) system, anin situmicroscopic imaging system. Broadly speaking, the SPC consists of three units: (1) an underwater, free‐space, dark‐field imaging microscope; (2) a server‐based management system for data storage and analysis; and (3) a web‐based user interface for real‐time data browsing and annotation. Combined, these components facilitate observations and insights into the diverse planktonic ecosystem. Here, we detail the basic design of the SPC and briefly present several preliminary, machine‐learning‐enabled studies illustrating its utility and efficacy.

     
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  6. Abstract

    Modern in situ digital imaging systems collect vast numbers of images of marine organisms and suspended particles. Automated methods to classify objects in these images – largely supervised machine learning techniques – are now used to deal with this onslaught of biological data. Though such techniques can minimize the human cost of analyzing the data, they also have important limitations. In training automated classifiers, we implicitly program them with an inflexible understanding of the environment they are observing. When the relationship between the classifier and the population changes, the computer's performance degrades, potentially decreasing the accuracy of the estimate of community composition. This limitation of automated classifiers is known as “dataset shift.” Here, we describe techniques for addressing dataset shift. We then apply them to the output of a binary deep neural network searching for diatom chains in data generated by the Scripps Plankton Camera System (SPCS) on the Scripps Pier. In particular, we describe a supervised quantification approach to adjust a classifier's output using a small number of human corrected images to estimate the system error in a time frame of interest. This method yielded an 80% improvement in mean absolute error over the raw classifier output on a set of 41 independent samples from the SPCS. The technique can be extended to adjust the output of multi‐category classifiers and other in situ observing systems.

     
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  7. Abstract

    The meroplanktonic larvae of many invertebrate and vertebrate species rely on physical transport to move them across the shelf to their adult habitats. One potential mechanism for cross‐shore larval transport is Stokes drift in internal waves. Here, we develop theory to quantify the Stokes velocities of neutrally buoyant and depth‐keeping organisms in linear internal waves in shallow water. We apply the analyses to theoretical and measured internal wave fields, and compare results with a numerical model. Near the surface and bottom boundaries, both neutrally buoyant and depth‐keeping organisms were transported in the direction of the wave's phase propagation. However, neutrally buoyant organisms were transported in the opposite direction of the wave's phase at mid depths, while depth‐keeping organisms had zero net transport there. Weakly depth‐keeping organisms had Stokes drifts between the perfectly depth‐keeping and neutrally buoyant organisms. For reasonable wave amplitudes and phase speeds, organisms would experience horizontal Stokes speeds of several centimeters per second—or a few kilometers per day in a constant wave field. With onshore‐polarized internal waves, Stokes drift in internal waves presents a predictable mechanism for onshore transport of meroplanktonic larvae and other organisms near the surface, and offshore transport at mid depths.

     
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  8. Abstract

    Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s−1vs. cm s−1) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.

     
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  9. Abstract

    Cross‐shore velocities in the coastal ocean typically vary with depth. The direction and magnitude of transport experienced by meroplanktonic larvae will therefore be influenced by their vertical position. To quantify how swimming behavior and vertical position in internal waves influence larval cross‐shore transport in the shallow (~ 20 m), stratified coastal waters off Southern California, we deployed swarms of novel, subsurface larval mimics, the Mini‐Autonomous Underwater Explorers (M‐AUEs). The M‐AUEs were programmed to maintain a specified depth, and were deployed near a mooring. Transport of the M‐AUEs was predominantly onshore, with average velocities up to 14 cm s−1. To put the M‐AUE deployments into a broader context, we simulated > 500 individual high‐frequency internal waves observed at the mooring over a 14‐d deployment; in each internal wave, we released both depth‐keeping and passive virtual larvae every meter in the vertical. After the waves' passage, depth‐keeping virtual larvae were usually found closer to shore than passive larvae released at the same depth. Near the top of the water column (3–5‐m depth), ~ 20% of internal waves enhanced onshore transport of depth‐keeping virtual larvae by ≥ 50 m, whereas only 1% of waves gave similar enhancements to passive larvae. Our observations and simulations showed that depth‐keeping behavior in high‐frequency internal waves resulted in enhanced onshore transport at the top of the water column, and reduced offshore dispersal at the bottom, compared to being passive. Thus, even weak depth‐keeping may allow larvae to reach nearshore adult habitats more reliably than drifting passively.

     
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